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Nucleus. 2018 Jan 1;9(1):171-181. doi: 10.1080/19491034.2018.1431081.

Differential staining of peripheral nuclear chromatin with Acridine orange implies an A-form epichromatin conformation of the DNA.

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a Latvian Biomedical Research & Study Centre , Ratsupites 1, Riga , Latvia.
b Institute of Biomedical Engineering and Nanotechnologies, Riga Technical University , Kalku iela 1, Riga , Latvia.
c Faculty of Biology, University of Latvia , Raina bulvaris 19, Riga , Latvia.
d Institute of Kardiology and Regenerative Medicine, University of Latvia , Raina bulvaris 19, Riga , Latvia.


The chromatin observed by conventional electron microscopy under the nuclear envelope constitutes a single layer of dense 30-35 nm granules, while ∼30 nm fibrils laterally attached to them, form large patches of lamin-associated domains (LADs). This particular surface "epichromatin" can be discerned by specific (H2A+H2B+DNA) conformational antibody at the inner nuclear envelope and around mitotic chromosomes. In order to differentiate the DNA conformation of the peripheral chromatin we applied an Acridine orange (AO) DNA structural test involving RNAse treatment and the addition of AO after acid pre-treatment. MCF-7 cells treated in this way revealed yellow/red patches of LADs attached to a thin green nuclear rim and with mitotic chromosomes outlined in green, topologically corresponding to epichromatin epitope staining by immunofluorescence. Differentially from LADs, the epichromatin was unable to provide metachromatic staining by AO, unless thermally denatured at 94oC. DNA enrichment in GC stretches has been recently reported for immunoprecipitated ∼ 1Kb epichromatin domains. Together these data suggest that certain epichromatin segments assume the relatively hydrophobic DNA A-conformation at the nuclear envelope and surface of mitotic chromosomes, preventing AO side dimerisation.  We hypothesize that epichromatin domains form nucleosome superbeads. Hydrophobic interactions stack these superbeads and align them at the nuclear envelope, while repulsing the hydrophilic LADs. The hydrophobicity of epichromatin explains its location at the surface of mitotic chromosomes and its function in mediating chromosome attachment to the restituting nuclear envelope during telophase.


DNA A-form; DNA structural test; LADs; NADs; acridine orange; epichromatin; nucleosome superbeads

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